Kathryn's Secret
by Jerilyn Elizabeth
Summary: The captain has a secret...will she be able to share it with the person that matters most? Kathryn/Chakotay
1. Chapter 1

For the record: _Voyager_ is not, and never will be, mine (though I wish that were different).

Location: New Earth

Kathryn Janeway's Personal Log…Supplemental:

We've been in the Delta Quadrant for 5 years now and I've never been more homesick than I am today. While I look forward to getting to my bridge most days, there are some days I would rather stay in my quarters and not come out. Being on the bridge with him sitting less than a foot from me is difficult, especially when I know I can't say anything to him. Lately, though, I've been thinking to hell with it and just tell him anyway. Just pin my heart to my sleeve and see what he thinks.

The one night stand with him six weeks ago could have ended in disaster, but we've both acted like professionals ever since. I wish I could get him out of my head! It would be so much easier than having my breath become heavy at the mere sight of him. I honestly hope that no one finds out, though I have the feeling that Tuvok and Seven already know with how sharp their senses are. Though I swear, if we come under one more severe attack by a species who just isn't willing to listen, I will tell him. I'll tell him everything and hope beyond hope that he understands…and that he wants me, too.

_Captain to the Bridge. All hands…Red Alert. Report to battle stations. I repeat, report to battle stations._

Damn it. Looks like my confession is going to come sooner rather than later. I hope you're ready Chakotay…for both of my secrets.


	2. Chapter 2

_**For the record: Voyager**_** is not, and never will be, mine (though I wish that were different).**

**Location: USS Voyager**

"**Report!" I snapped as I walked briskly onto the bridge.**

"**Captain, it looks as though the Vidiians are wanting to harvest more organs," Tuvok replied, sounding slightly amused. "Shields are holding."**

"**Do we have warp?" I asked Ensign Tom Paris. **

"**Aye, captain," he said. "Do you think we should try to disable their weapons before we run, though?"**

"**Of course," I said dryly. "Tuvok, aim for their weapons array and fire."**

"**Yes, Captain," Tuvok replied and followed my orders with perfect precision. I heard the phasers fired with perfect aim. "Their weapons have been disabled."**

"**Tom, Warp 8," I said, settling into my chair. "I want to be at least three light years away before I will feel safe. Engage."**

"**Aye, ma'am," he said, keeping his eye on the controls. **

**I stayed on the bridge during those three light years, staying at red alert until we were far enough away.**

"**Stand down red alert," I said, more relaxed that I was before. "I'll be in my ready room."**

**I started walking towards my ready room, then slightly hesitated when I remember the promise I had made myself in my personal log.**

"**Chakotay, will you join me, please," I said without the hesitation I was feeling. "There is something that I need to discuss with you."**

"**Aye, Captain," he replied, following me.**

"**Tuvok, you have the bridge," I said.**

"**Yes, captain," he replied, temporarily taking my chair.**

**As we strode into my ready room, I wondered how I was going to say what I needed to say to him. How should I put it? Should I draw it out or should I just put it out there and hope for the best? **

**After the door hissed closed behind us, I gave the computer the order to make sure we were left in complete privacy.**

"**Computer, security protocol on my ready room, Janeway-alpha-1," I said casually.**

"_**Security protocol in place.**_**"**

"**Captain?" I hear the unasked question in his voice.**

"**I need to discuss something with you and I don't want anyone just walking by to hear what I have to say. And you're under orders to not repeat anything I'm about to tell you. Is that understood?"**

"**Yes, Captain," the confusion in his voice somehow makes this funnier and I want to giggle, but I know I have to repress it if I'm going to get out what I need to tell him. **

"**Chakotay, there's something I've been meaning to tell you for a long time…" I let the suspense build just a few moments more before I spill my guts. I look him straight in the eyes.**

"**I love you, Chakotay, with all my heart."**

**I don't think I've ever seen his jaw drop so quickly.**

_**Reviews are always welcome, as are critiques! **_


	3. Chapter 3

Chapter 3

For the record: _Voyager_ is not, and never will be, mine (though I wish that were different).

Location: USS Voyager

"You love me?" Chakotay whispered. "But-but Michael…"

"Michael is a holographic character made of photons and force fields," I said gently. "Yes, I care about him, but he can't give me what you've already given me: your love in return."

"Oh, Kathryn," Chakotay whispered as he looked deep in my eyes and cupping my face in his hands. "I do love you. I have since we left New Earth."

Chakotay rested his forehead against mine and we just stood there for a moment with our eyes closed. I knew I had to tell him the other part of my secret; I knew I couldn't keep it from him any longer.

"Chakotay, there's something else that I need to tell you," I said hesitantly, pulling back from him slightly. " I'm just not sure how to say it…"

"Is everything all right, Kathryn?" Chakotay asked lightly, concern in his warm, dark brown eyes.

"Everything is fine," I assured him. "I do have some wonderful news, though."

"What kind of wonderful news?" he asked, a glimmer of something starting to shine in his eyes.

"In about seven and a half months you and I are going to be parents," I whispered, not daring to look up at him, though I am normally fearless.

"Parents? You're pregnant?" he whispered. My curiosity got the best of me and I peeked a look at Chakotay's face. There was nothing there but love, happiness, and admiration. Then he shouted, "Parents!"

Chakotay grabbed me, spun me in a quick circle, and put me back down, though looking a little worried.

"Morning sickness?" he asked.

"None," I answered truthfully. "To tell you the truth, I didn't even know that I was pregnant until I went to the doctor for a migraine that wouldn't go away. Don't worry," I said hastily as I saw his look of concern. "The doctor said migraines are normal, but he did give me medicine to counteract the affects."

"Thank the spirits," he breathed. " And…"

"There's no sign of the crazy gene that had affected your family," I interrupted before he could finish his sentence. "Don't worry, the doctor is keeping a close eye on that, too, as well as me and the baby."

"So the doctor knows?" Chakotay asked, sounding slightly irritated.

"He did run a DNA scan," I admitted. "But he promised complete doctor-patient confidentiality. He won't breathe a word until ordered to."

"Good," Chakotay replied softly, placing his hands on my still-flat stomach, though we both knew that it wouldn't stay that way for long. He pulled me into a gentle embrace.

"So who should we tell first?" he asked as he rested his chin on my head.

"Maybe we should make a ship-wide announcement," I joked. "Imagine what Tom and B'Elanna would say."

"Imagine what Neelix would say," Chakotay joked back. "You know he would probably offer to be godfather."

"I know," I replied, speaking seriously. "But I have someone else in mind for that job, if you're amenable."

"Who?" Chakotay asked curiously as we sat down on the bench that was framed by stars.

"Tom Paris," I replied, resting my head against his shoulder while he wrapped his arm around me.

"That sounds fine to me," he said, pulling me close. "Tom sometimes acts like a big kid himself."

I quickly sat up, remembering that we were still on duty.

"We had better get back to the bridge or Tuvok might send a search party after us," I said slowly. I was so comfortable that I didn't want to get up. "And remember, don't say anything to anyone. That's an order, Commander."

"Aye, Captain," he joked. "Until tonight, then?"

"Tonight," I agreed with a smile.

"Computer, disengage security protocols, Janeway-alpha-1."

"_Security protocols disengaged."_

"Doctor to the Captain, please respond!"

"He sounds kind of annoyed," I remarked before tapping my combadge.

"This is Janeway," I said, slightly amused. "What do you need, Doctor?"

"Finally! I've been trying to contact you for almost five minutes!" the Doctor snapped, sound more than slightly annoyed. "I need to see you in Sickbay as soon as possible."

"On my way, Doctor," I replied as Chakotay and I briskly walked onto the bridge. "Commander, you have the bridge."

"Aye, Captain," Chakotay said, looking and sounding completely impassive.

As I entered the turbo lift, I wondered what the Doctor needed that was so important. Since I didn't have long to wait, I pushed it from my mind and started thinking about something that was more enjoyable.

"Sickbay," I said as the doors hissed closed.

When I finally reached Sickbay, the Doctor looked extremely relieved.

"Captain, finally!" he said, quickly closing the distance between us. "I was started to wonder…but never mind. I was studying the scans I took of you yesterday, but I need to scan you again just to be sure of my conclusions."

"What conclusions are those?" I asked, curiosity filling my voice.

"Let me scan you to confirm my hypothesis, then I will tell you, no before," the Doctor said stubbornly.

"As you wish," I concede as I laid down on the biobed. I decided to be a good patient and tried to patiently wait as the Doctor performed his scans.

"As I thought," the Doctor replied as he finally finished his scans.

"Well, Doctor? What conclusions did you reach?" I ordered.

"You are indeed pregnant, Captain," the Doctor smiled. "With twins. Congratulations."

I fainted.


	4. Chapter 4

Chapter 4

For the record: _Voyager_ is not, and never will be, mine (though I wish that were different).

Location: USS Voyager

"Kathryn," I heard a foggy voice say insistently. "Kathryn!"

I slowly opened my eyes to discover that I was once again laying on the biobed and that I was not alone.

"Thank goodness!" Chakotay breathed a sigh of relief. "When the doctor called me to Sickbay, I didn't know what to expect."

"How long…?" I let my unfinished question trail off as I slowly tried sitting up.

"Only a few minutes," the Doctor assured while running a scan to make sure I really was okay. "I imagine it was the shock of the news."

"News? What news?" Chakotay demanded, giving the Doctor a look. "Is everything okay?"

"Everything is better than okay," the Doctor replied, putting his medical tricorder away. "But I'll let the Captain tell you."

"Kathryn?" he looked at me with concern.

"It twins, Chakotay," I said, looking the father of my children in the eyes. "I'm pregnant with twins."

I watched the shock of the news slowly spread across his features. He searched my eyes for some sort of deception, and in finding none, wordlessly took the padd the Doctor had just handed me.

"Twins," he repeated, his voice full of wonder. He wrapped my up in a gentle embrace.

"You'll be able to find out the sexes in about six weeks if you'd like to," the Doctor said, oblivious to the tender exchange.

"Yes, definitely," I replied, the smile on my face growing in intensity, though questions were racing through my mind.

"I'll want to see you on a weekly basis for the first two trimesters, then twice a week during the third trimester so I can supply you with prenatal vitamins. These visits are not optional," the Doctor said, glaring at me because he knew my record of keeping Sickbay appointments. "I'll see you next week. Until then, you are free to go back on duty."

"Thank you, Doctor," I replied, slowly standing. I silently vowed to be more careful from then on.

"Oh, and Captain?" the Doctor injected. "That means no more training with the Klingons on the holodeck with the safety protocols off."

I blushed, knowing another secret had been revealed.

"Yes, Doctor," I said, straightening my uniform. "I'll be returning to the bridge now."

As Chakotay and I made our way back to the bridge my mind was at warp 9. There were more unanswered questions now than there were before this meeting with the doctor. For the first time in my life, I had no idea what to do. Fortunately, I wasn't alone.

"So what are we going to do?" Chakotay asked softly as we walked down the corridor. I quickly glanced at him and saw the unconditional love I had always craved.

"I have absolutely no idea," I replied as we entered the turbo lift.

"Bridge," Chakotay ordered the computer. He looked at me, his eyes full of admiration with a touch of concern. "We're not going to be able to keep this a secret for as long as we had hoped."

"I know," I sighed as I lightly pinched the bridge of my nose between my fingers. "But until I'm ready, don't breathe a word of this to anyone. That's an order."

"Aye, Captain," he said just as the doors of the turbo lift open to reveal the bridge.

The scene we walked into was one that I would not soon, if ever, forget.

_As always, reviews are welcome. And thank you to those who have!_


	5. Chapter 5

Chapter 5

Author's Note: Star Trek Voyager is not mine (though I wish that were different)

Ballons, flowers and streamers filled the bridge. The entire bridge crew and the regular senior staff plus the Doctor, Neelix,a nd Seven had risen to their feet to applaud their Captian and First Officer. I blushed redder than a ripened Talaxian tomato. I peaked over to see the look on Chakotay's face and it was even redder than my own. I was about to ask who had spilled the beans until I saw little Naomi Wildman peak around from behind Harry Kim. She looked worried, like she was going to get in trouble for telling, but I gave her a smile to ensure her that everything was okay.

"Congratulations, Captain!" was the sentiment that we heard from around the room.

"So do you know what it is, yet, Captain?" B'Elanna asked, giving me a bigger smile than I had ever seen before.

"No, we don't know what sex _they_ are yet," I replied, putting specially emphasis on the word "they."

" 'They?,' Captain?" Neelix asked, sound a bit confused. I couldn't blame him. Chakotay and I were confused ourselves.

"We're having twins," I smiled widely. "Not one baby, but two."

The shell-shocked look on everyone's faces was worth dropping the bomb all at once. Then the applause started again.

"What are you due, Captain?" Harry asked, his young eyes full of wonder.

"In about seven and a half months, but from what I know of twin births, they'll probably want to come out at about the six and a half to seven month mark," I answered, knowing the Doctor would probably wait as long as he could before I gave birth.

"And with a doctor like me, you couldn't be in better hands," the Doctor boasted lightly. I smiled. "And from what I can see, the babies are healthy and doing fine."

"Thanks, Doctor," I said taking my Captain's seat while Chakotay took the seat to my left. "I promise we'll have a big party at Sandrine's after duty shift, but right now we need to get back to work."

"Aye, Captain," was the consensus, the Doctor, Neelix, and Seven all heading back to their respective stations. The bridge crew offered me another congratulation and then gave their attention to the view screen and the sensor readings. I hoped beyond hope that nothing anomalis would happen for the next few months, but I also knew that the possibility of everything being completely perfect was rather small, too, especially being in the unexplored Delta Quadrant.

Duty shift ended normally and I had a few minutes to get ready for the party that I promised all of them in Holodeck 2. So for a few minutes, instead of going to my quarters, I activated Holodeck 1 and started the program that I had been running before I told Chakotay that I loved him and that I was pregnant. There was something else that I needed to take care of before I attended the party; something that was eating me up inside and that I had to know the answer to.

"Security protocol Janeway-alpha-1," I said as I walked on to the holodeck. "Computer place a force field around this room, level 10. Activate program Janeway-pi-alpha."

The latest version of the emergency medical hologram appeared, the EMH Mark 4, and was only programmed with the information that I needed him to know: genetics and DNA sequencing and comparing.

"Hello, Doctor," I said softly. "What have you found?"

"I have reached my conclusions. Your initial suspicion was correct, Captain Janeway," the hologram replied, looking me straight in the eyes.

"And your conclusions are?" I asked stiffly, wringing my hands in front of me.

"Commander Chakotay is not the father of your baby."


	6. Chapter 6

_**I apologize for the long delay...my college classes have been kicking my butt! I hope this makes up for the absence. **_

"The babies aren't Chakotay's?" I asked in a whisper. I felt light-headed, almost to the point of fainting. I leaned against one of the holographic biobeds.

"Excuse me, Captain," the EMH Mark 4 said lightly. "Did I hear you say 'babies,' as in more than one?"

"Yes, doctor," I said in a shaky voice. "It was confirmed this morning by my ship's doctor that I am carrying twins."

"If I may, Captain, I would like to check the genetic marker on both babies to be sure that they have to same father," the holographic EMH Mark 4 replied.

"Doctor?" I looked at him confused.

"In rare cases when a woman is carrying fraternal twins, it is possible for the two eggs to be fertilized by two different men," the EMH Mark 4 explained. "Though rare, it is still possible."

"By all means, doctor, please go ahead," I said, quickly laying down on the biobed.

I knew the procedure would take a couple of minutes, so I tried to get my mind to relax though I knew that was easier said than done. I ran over the events of the past couple weeks and berated myself for having so much to drink that I couldn't remember what happened the night I got pregnant. The EMH Mark 4 made no noise as he continued with his work. I wondered how I was going to break it to Chakotay that the baby, or babies, were not his.

"I've finished, Captain," the EMH Mark 4 said, lowering the hood from the biobed.

"And?" I asked in a frightened voice.

"You are indeed carrying twins," he confirmed. "But unfortunately, neither baby is Chakotay's."

"What?" I tried to exclaim, though it only came out as a whisper. I tried to compose myself enough to be heard. "Who is the father then?"

"Lieutenant Tom Paris."

"How can that be?" I was shocked. How in the hell had Tom Paris impregnated me? What happened that night that I could remember? With more answers only came more questions. How in the hell was I going to figure them out. I needed to talk to both Tom and Chakotay, separately because who knows what Chakotay would do to Tom if he found out, and I needed to do it soon.

I took a few deep breaths to calm and compose myself. I had a party to attend and I didn't want people thinking that there was something wrong, even though there was. I wanted to keep this my secret for now.

"Thank you, Doctor," I said to the EMH Mark 4 as I slowly got up. "I will keep you updated as to what happens."

"You're welcome, Captain," he said. "Though as long as you continue to see your ships doctor, you should have nothing to worry about."

"Computer, program," I said grimly, taking one final deep breath before I released the security protocols. I put on my game face, heaven knew I was going to need it before this night was through. Tonight I was going to find out the answers to my questions.

But first I had a party to attend.

I strode into the next holodeck like I didn't have a care in the world. As I walked up to Chakotay, the room burst into applause. Banners and streamers were hanging everywhere and little Naomi was holding a dozen roses. Even the Doctor was there to offer his congratulations. I gave as wide of a smile as I could give as Chakotay wrapped his arm around me.

"Congratulations, Captain!" Neelix rushed over to me, handing me a mug of my all time favorite drink, black coffee.

"Now Neelix, according to medical research, the Captain shouldn't have too much coffee," the Doctor warned. "It could mess with the babies heart rates." Seeing the look on my face, he amended his statement. "Though one mug a day shouldn't hurt you, so long as you keep it at only one."

"And what am I supposed to do after that?" I asked, worried how I was going to stay awake during the later part of the shift.

"I recommend tea, Earl Grey to be precise," the Doctor said.

"Okay, tea I can live with," I smiled again.

Everyone laughed and the party went on like normal. I pretended through the whole night that nothing was wrong. Hell, I should have won a reward for the way I acted. The night still moved slowly though, too slowly for me. I wanted to talk to Chakotay, but knew that I had to wait before I could. What in the hell was I going to say?

As the party ended and everyone either went to their shift or the quarters, I stayed to help clean up, though Neelix and Chakotay both told me that I couldn't and shouldn't.

As we were walking to my quarters I knew the time had come. I had to tell Chakotay. I steered him toward Sick Bay

"Is something wrong?" Chakotay asked, a little worried.

"No, there's nothing wrong, I just want to go see the Doctor before I go to bed and check to see if everything is ok," I replied hating what I was going to do next.

"Okay," he said. He still sounded worried.

As we walked into Sick Bay, the Doctor looked up from his work.

"Ah Captain," he sounded pleased. "How are you doing this evening after the party?"

"I'm doing fine," I said. "But there is something that I need you to check."

"What's wrong, Captain?" the Doctor sounded concerned.

I handed him the PADD that the EMH Mark 4 had transferred his data to.

"I need to you to look at and verify this information," I said in a firm voice. "And don't say another word until you do."

"But Captain-"

"That's an order," I said in my most authoritative voice.

"Yes, ma'am," he said.

The Doctor looked at the PADD, kept his poker face, and asked me to lay down on the biobed. I did as asked, which is rare for me, and settled all the answers in my mind. The Doctor looked up from the PADD and gave his infamous look.

"The information on here is correct," he said.

"What information?" Chakotay asked. "Kathryn, what in the hell is going on?"

I looked at my lover straight in the eyes, tears forming in mine.

"When I woke up the morning after our tryst, things were more out of place than I remembered them," I began, the tears slowly sliding down my cheeks. "Like someone had thrown things around after getting angry. The only thing that I remembered was being with you and I knew that you hadn't done that, so when I found out that I was pregnant, I started a program that I had made for Samantha when we found out that she was pregnant. The doctor there and the Doctor here just agreed in their diagnoses."

"Which is what Kathryn?" Chakotay pleaded, his large warm hands around mine.

"The twins aren't yours," I whispered. "I was raped after you left that night. I found out by who right before the party."

"Who did this to you, my love?" I could hear his voice smoldering.

I started crying outright.

"Tom Paris."


End file.
